Hierarchical alignments with the <em>Helianthus annuus</em> genome as reference

Gene Search

Species

Gene ID

Example:

Or, Query Sequence

Example:

Hierarchical alignments with the Helianthus annuus genome as reference

Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Helianthus annuus as a reference, and by comparing homologous gene locus maps and Ks values between Helianthus annuus and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We constructed a 40×70, 843 macro-matrices.

Query Sequence

Or, Gene ID

Species

Hean_1	Cobi_1	Bial_1	Bial_2	Dapi_1	Dapi_2	Hetu_1	Hetu_2	Hetu_3	Amtr_1	Smso_1	Smso_2	Taer_1	Fro_1	Fso_1	Ftr_1	Fra_1	Fli_1	Stre_1	Mimi_1	Hean_2	Cobi_2	Bial_3	Bial_4	Dapi_3	Dapi_4	Hetu_4	Hetu_5	Hetu_6	Amtr_2	Smso_3	Smso_4	Taer_2	Fro_2	Fso_2	Ftr_2	Fra_2	Fli_2	Stre_2	Mimi_2
Hean17g04501	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04502	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04503	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04504	Cobi5g02855	.	Bial9g02669	.	Dapi21g00144	Hetu50g03541	Hetu51g03905	Hetu49g03843	Amtr10g04212	.	Smso21g01339	.	.	.	.	.	.	Stre11g00180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04505	.	.	.	Dapi5g00097	Dapi21g00145	Hetu50g03540	Hetu51g03904	Hetu49g03842	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04506	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04507	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04508	Cobi5g02853	.	.	.	.	.	.	.	Amtr10g04218	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04509	.	.	.	.	.	.	.	Hetu49g03839	.	.	Smso21g01343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Hean17g04510	.	.	.	Dapi5g00099	Dapi21g00147	Hetu50g03534	Hetu51g03900	Hetu49g03838	Amtr10g04222	Smso4g01379	.	.	.	.	.	.	.	.	Mimi2g00088	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

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Gene_GFF

Chromosome	Start	End	Strand	Old_gene	Gene	Num
10	97988418	97992189	-	AtrifAMIRv0_Chr10g0665861	Amtr10g04212	4212
10	98211176	98212824	+	AtrifAMIRv0_Chr10g0665921	Amtr10g04218	4218
10	98251935	98253128	-	AtrifAMIRv0_Chr10g0665961	Amtr10g04222	4222
9	71581225	71584507	+	g77049.t1	Bial9g02669	2669
5	79160512	79162854	-	h2tg000020l_1.g9927.t1	Cobi5g02853	2853
5	79202697	79205530	+	h2tg000020l_1.g9925.t1	Cobi5g02855	2855
5	2304771	2308568	+	h1tg000132l.g124154.t1	Dapi5g00097	97
5	2337536	2338496	-	h1tg000132l.g124156.t1	Dapi5g00099	99
21	2938795	2941798	-	h1tg000096l.g113418.t1	Dapi21g00144	144
21	2945549	2949359	+	h1tg000096l.g113417.t1	Dapi21g00145	145
21	2973513	2974646	-	h1tg000096l.g113415.t1	Dapi21g00147	147
17	193311380	193312163	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831001	Hean17g04501	4501
17	193315147	193317112	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831011	Hean17g04502	4502
17	193320321	193324830	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831021	Hean17g04503	4503
17	193328868	193334066	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831031	Hean17g04504	4504
17	193338615	193339382	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831051	Hean17g04505	4505
17	193339968	193341870	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831061	Hean17g04506	4506
17	193357431	193358713	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831101	Hean17g04507	4507
17	193475113	193477161	+	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831111	Hean17g04508	4508
17	193533977	193535492	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831131	Hean17g04509	4509
17	193588882	193590096	-	gnl\|WGS:MNCJ\|mrna.Hean1vXRQr2_Chr17g0831141	Hean17g04510	4510
49	221630257	221631173	+	>Htub.h1tg001001l.g570.t1	Hetu49g03838	3838
49	221733892	221734801	+	>Htub.h1tg001001l.g571.t1	Hetu49g03839	3839
49	221927896	221931149	-	>Htub.h1tg001001l.g574.t1	Hetu49g03842	3842
49	221935165	221939838	+	>Htub.h1tg001001l.g575.t1	Hetu49g03843	3843
50	206585400	206586312	+	>Htub.h1tg000531l.g334.t1	Hetu50g03534	3534
50	206809237	206812524	-	>Htub.h1tg000531l.g340.t1	Hetu50g03540	3540
50	206816560	206820804	+	>Htub.h1tg000531l.g341.t1	Hetu50g03541	3541
51	228057852	228058775	+	>Htub.h1tg000558l.g131.t1	Hetu51g03900	3900
51	228319893	228323170	-	>Htub.h1tg000558l.g135.t1	Hetu51g03904	3904
51	228327234	228332272	+	>Htub.h1tg000558l.g136.t1	Hetu51g03905	3905
2	2427731	2429148	+	KAD7116504.1	Mimi2g00088	88
4	18830979	18832225	-	KAI3818232.1	Smso4g01379	1379
21	14219063	14223581	-	KAI3731545.1	Smso21g01339	1339
21	14306726	14307727	-	KAI3731549.1	Smso21g01343	1343
11	5712967	5715473	+	Streb.11G001800.1	Stre11g00180	180

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